I`m not sure about employing microscopic methods for this purpose. If you want to investigate the effect of microwave on molecular changes in pure substances, I recommend using FTIR method before and after microwave irradiation.
Use FESEM - it can do absolutely everything - from taking high quality pics at low vaccum - thus minimizing sample preparation - it can also do elemental analysis - which I suppose would be important for food analysts.
It is absolutely impossible. Using optical microscopy we can see objects rather not smaller than 0,5 μm. It means that we can see for example elements of cell structures. Using electron microscopy we can see structures of dimension of nanometers. Microscopy is often used for investigation of so called supermolecular structure.
Molecular structure means atoms forming a given substance as well as the nature of connections between individual atoms. Molecular structure is examined using elemental analysis, spectroscopy (IR, NMR, MS) but not using microscopy.
I had not mentioned optical microscope but FE - SEM. In this you can do material charecterisation also along with traditional scanning, see the following webpages for details:
Watching ongoing discussion, I can see that there is a huge misunderstanding what does exactly mean molecular structure. As I mentioned previously, molecular structure means atoms and connections between them. For example, molecular structure corresponds to primary structure of proteins. Using even electron microscopy of resolution of few nanometers you can see only secondary structure of proteinds. Atoms have diameters of the level of magnitude of picometres but not nanometers.